There is many a board layout that simply lacks the room for a top mounted heatsink and fan, it would be impractical to have one reversed. There will often be a CPU slot, memory, something, within half an inch of the top slot. There is also the exhaust out the back, the porting is south of the PCB, not north. Card orientation has been universal, or near to it, since before video cards. They're just doing it the same way they always have, with the components on the underside, which most definitely does not help the typical expansion card cool better.

Actually... WAY back in the day, tower cases were rare & motherboards were mounted horizontally so it'd be parallel to your desk. This would leave the add-on cards such as Modem/Sound Card/Video Cards to be standing straight up & down.

Cooling was really neglected in design work up until probably the late 90s "Yes early/mid 90s CPUs would have passive cooling"

There are some cases out there that actually flip the board upside down, the only issue is the heat from the CPU rises into add-on cards with that design, as well as the BTX motherboard standard which fizzled out due to lack of proper scaling when it came to cooling. -- BTX died about 10 or so years ago.